请教能量最小化和正式模拟报错问题

BlinBlin

各位老师好，想请教大家三个问题：
1.在能量最小化过程中，没有到达我的设定值程序就停止了，请问该怎么处理？
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 100 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.


Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)


writing lowest energy coordinates.


Steepest Descents converged to machine precision in 15061 steps,
but did not reach the requested Fmax < 100.
Potential Energy  = -1.6876581e+06
Maximum force     =  5.6473102e+02 on atom 1462
Norm of force     =  3.4225984e+00



GROMACS reminds you: "PHP is a minor evil perpetrated and created by incompetent amateurs, whereas Perl is a great and insidious evil, perpetrated by skilled but perverted professionals." (Jon Ribbens)


2.在正式模拟过程中会报错，有许多LINCS WARNING，最后提示表明系统没有很好的平衡，是不是因为第1个问题中能量最小化没有做好？
Step 50797376, time 101595 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000032, max 0.000336 (between atoms 2305 and 2303)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length


Step 50797376, time 101595 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000060, max 0.001279 (between atoms 2289 and 2283)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
   2285   2286   45.9    0.0973   0.0973      0.0973
   2285   2286   45.9    0.0973   0.0973      0.0973

………………（有许多LINCS WARNING）
Fatal error:
1 particles communicated to PME rank 9 are more than 2/3 times the cut-off out
of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.


3.在问题2中，续算也能继续算下去，只是后续还会报错，但续算几次后就不报错了。请问续算的结果是否可信？

sobereva

既然“续算几次后就不报错了”，大概率不是拓扑文件有问题，继续跑下去就完了。


MD初期可以用很小的步长让MD不容易出现不稳定，比如0.5 fs跑个几百ps，让体系一定程度弛豫，然后再改用常见的2 fs步长继续跑
参考下文的讨论
http://sobereva.com/soft/Sobtop#FAQ8

BlinBlin

sobereva 发表于 2024-2-15 13:35
既然“续算几次后就不报错了”，大概率不是拓扑文件有问题，继续跑下去就完了。

[/backcolo ...

好的好的，谢谢sob老师！